SlicerOpenNav

Open source tools for surgical navigation built as a 3D Slicer extension.

Overview

SlicerOpenNav (also known as OpenNav) provides a complete workflow for image-guided surgical navigation, including:

• Patient Management: DICOM import, case organization, and automatic session saving/loading
• Surgical Planning: Skin and target segmentation, trajectory planning, and anatomical landmark definition
• Tool Calibration: Pivot and spin calibration for tracked surgical instruments
• Patient Registration: Landmark-based and surface-based (ICP) registration to align patient anatomy with preoperative imaging
• Real-time Navigation: Live instrument tracking with multi-planar reformatted views following the pointer tip

Features

• Guided step-by-step workflow with validation at each stage
• OptiTrack optical tracking integration via PLUS toolkit
• Automatic case saving and session recovery
• Customizable anatomical landmark selection
• Surface tracing for registration refinement
• Multiple navigation view layouts (6-up, 2-up)

Requirements

• 3D Slicer (version 5.0 or later recommended)
• PLUS toolkit for optical tracking support
• OptiTrack camera system (or compatible tracking hardware)

Slicer Extension Dependencies

• SlicerOpenIGTLink
• SlicerIGT

Installation

From Extension Manager

(Coming soon)

From Source

1. Clone this repository:

   git clone https://github.com/NousNav/SlicerOpenNav.git

2. Build as a Slicer extension:

   mkdir SlicerOpenNav-build && cd SlicerOpenNav-build
   cmake -DSlicer_DIR=/path/to/Slicer-build/Slicer-build ../SlicerOpenNav
   cmake --build . --config Release

3. Or load directly in Slicer for development:

   • Open Slicer
   • Go to Edit → Application Settings → Modules
   • Add the module directories to "Additional module paths"
   • Restart Slicer

Usage

Workflow Overview

1. Patients: Load DICOM images or open an existing case
2. Planning:
   • Segment the skin surface
   • Segment the target anatomy
   • Define the surgical trajectory (entry and target points)
   • Place anatomical landmarks for registration
3. Registration:
   • Connect and position tracking hardware
   • Perform pointer pivot and spin calibration
   • Collect landmark points on the patient
   • Trace the skin surface for registration refinement
   • Verify registration accuracy
4. Navigation: Track instruments in real-time with image guidance

Data Storage

Cases are automatically saved to ~/OpenNav/Cases/{case_name}/ and can be reopened from the Patients screen.

Modules

Module	Description
Home	Main application interface and workflow orchestration
Patients	DICOM loading and case management
Planning	Segmentation and trajectory planning
Registration	Calibration and patient-to-image registration
Navigation	Real-time tracking and visualization
LandmarkManager	Anatomical landmark handling
OptiTrack	Optical tracking hardware integration
OpenNavUtils	Shared utilities and helpers

Contributing

Contributions are welcome! Please feel free to submit issues and pull requests.

Development

Pre-commit Hooks

This project uses pre-commit with ruff for linting and formatting:

pip install pre-commit
pre-commit install

Git Blame

To ignore formatting commits in git blame:

git config blame.ignoreRevsFile .git-blame-ignore-revs

License

This project is licensed under the Apache License 2.0 - see the LICENSE.txt file for details.

Acknowledgments

• Developed by Kitware Inc.
• Built on 3D Slicer
• Tracking integration via PLUS toolkit

References

• 3D Slicer Documentation
• PLUS toolkit Documentation